kraken2 vs krakenuniq

Question

[pinheirofabiano]

I'm starting a metagenomics project, but I'm in doubt if Kraken 2 is better than Krakenuniq or not.

Can you explain me the differences and help to choose?

many thanks, Fabiano

Answer 1

[Haci]

I had the same question a while back and made use of this excellent post from the maintainers. Quoting from there:

However, it [Kraken2] has a tiny false-positive rate (erroneously assigning a read to a species) that KrakenUniq does not have. This means that for diagnosis of infections, where the goal is to identify a very small number of reads (often just a few dozen out of millions), users should use KrakenUniq.

[pinheirofabiano]

what's the difference between them? what's a unique k-mer?